Longitudinal analysis of Salmonella Kentucky genomes from a long-term dairy herd epidemic reveals potential mechanisms of strain succession

Authors: SEON WOO, KIM - University Of Maryland; SALAHEEN, SERAJUS - University Of Maryland; Van Kessel, Jo Ann; Haley, Bradd

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 4/16/2019
Publication Date: 6/21/2019
Citation: Seon Woo, K., Salaheen, S., Van Kessel, J.S., Haley, B.J. 2019. Longitudinal analysis of Salmonella Kentucky genomes from a long-term dairy herd epidemic reveals potential mechanisms of strain succession. American Society for Microbiology. p. 1.

Interpretive Summary:

Technical Abstract: A multi-year outbreak of Salmonella enterica subsp. enterica serovar Kentucky was observed in a dairy herd that was enrolled in a longitudinal study where feces of asymptomatic dairy cattle were sampled intensively over an eight-year period. The aim of this work was to characterize the heterogeneity in S. Kentucky genomes isolated over the course of an outbreak and to investigate genomic polymorphisms that coincide with succession of S. Kentucky strains isolated from cows in the US. S. Kentucky isolates that were isolated from a dairy farm in Pennsylvania between 2004 and 2012 were sequenced on an Illumina MiSeq sequencer for 2 × 151 cycles. Single nucleotide polymorphisms (SNPs) were identified using Parsnp and the presence/absence of protein-coding genes was investigated using GET_HOMOLOGUES. Association and invasion assays were performed to investigate the interactions between the S. Kentucky isolates with the cultured bovine cell-line, MacT. A phylogenetic analysis indicated that the S. Kentucky genomes from the dairy farm strains were distinct from the publicly-available genomes of poultry strains. Three distinct clades of S. Kentucky were identified (clades K, A1, and A2) during the course of the study, suggesting three separate lineages of S. Kentucky were present at different times. Isolates from clade K were recovered between 2004 and 2006, clade A1 strains were isolated from the herd between 2005 and 2011, and were replaced by clade A2 which was isolated from 2009 to the end of the study in 2012. Clades A1 and A2 were more closely related to each other than they were to clade K. Genomic heterogeneity between the clades helped identify regions of the S. Kentucky genome, most notably an Hha virulence repressor and transcriptional regulators that may be involved with colonization of the bovine intestine and could play a major role in competition between highly similar strains. Association-invasion assays with cultured bovine epithelial cells demonstrated a significant difference in the invasiveness of S. Kentucky based on clades (and sequence types), that suggested a clade-specific immune response in the host may have played a role in the observed succession of strains. This study describes the dynamics of an S. enterica outbreak in a dairy herd over an eight-year period and indicates that long-term, asymptomatic outbreaks are more complex than previously understood. Further, within-serovar genomic polymorphisms may be partially associated with strain succession during long-term outbreaks.